As you indicated, these doors you bought are prehung to save you all the trouble of doing that. Cutting on the top of the doors means you have to cut new hinge and face plate mortises and rehang the door. Maybe more work than you want to take on. You would also be altering the height of the door knobs. If those are the pre-primed 6 panel prehung doors of the home cheapo variety, they probably shouldn't splinter like a plywood faced door but scoring won't hurt as well as using masking tape and cutting through the tape. After 2 years of rebuilding, don't cobble it up now so my vote still goes with cutting the headers. By the way, we typically hang a door about 1 1/4" above the unfinished floor so it will swing above most carpet and tile.